lyse analysis script demonstrating some Run methods for example_IMAQdx_remote

rpanderson · rpanderson · commit f13357c15e7a · 2020-06-22T17:44:36.000+10:00
diff --git a/labscript_profile/default_profile/userlib/analysislib/example_apparatus/example_IMAQdx_remote.py b/labscript_profile/default_profile/userlib/analysislib/example_apparatus/example_IMAQdx_remote.py
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+import lyse
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+# Is this script being run from within an interactive lyse session?
+if lyse.spinning_top:
+    # If so, use the filepath of the current shot
+    h5_path = lyse.path
+else:
+    # If not, get the filepath of the last shot of the lyse DataFrame
+    df = lyse.data()
+    h5_path = df.filepath.iloc[-1]
+
+# Instantiate a lyse.Run object for this shot
+run = lyse.Run(h5_path)
+
+# Get a dictionary of the global variables used in this shot
+run_globals = run.get_globals()
+
+# Extract the images 'before' and 'after' generated from camera.expose
+before, after = run.get_images('camera', 'comparison', 'before', 'after')
+
+# Compute the difference of the two images, after casting them to signed integers
+# (otherwise negative differences wrap to 2**16 - 1 - diff)
+diff = after.astype('int16') - before.astype('int16')
+
+# Plot the row-wise mean of each image
+plt.plot(before.mean(axis=0), label='before')
+plt.plot(after.mean(axis=0), label='after')
+plt.xlabel('pixel coordinate (column)')
+plt.ylabel('counts')
+
+# Label the plot with a unique string representing the shot
+plt.title(Path(run.h5_path).name)
+
+# Plot adornments
+plt.legend(loc='lower left')
+plt.grid()
+
+# Show the plot
+plt.show()
+
+# Compute a result based on the image processing and save it to the 'results' group of
+# the shot file
+result = diff.std()
+run.save_result('foobar', result)
